X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fproject%2FJalview2xmlTests.java;h=79d622c6e068065de8cbf53c2c65a71b0bdadf9e;hb=refs%2Fheads%2Ffeatures%2FJAL-1953_Archeopteryx_with_Jalview_2_11_2;hp=f5044bb3df5db11d161b3d84e5946f95d5d185ea;hpb=74393b51f368cb9f58589472d432a433d9c4386d;p=jalview.git diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java index f5044bb..79d622c 100644 --- a/test/jalview/project/Jalview2xmlTests.java +++ b/test/jalview/project/Jalview2xmlTests.java @@ -27,6 +27,22 @@ import static org.testng.Assert.assertNull; import static org.testng.Assert.assertSame; import static org.testng.Assert.assertTrue; +import java.awt.Color; +import java.io.File; +import java.io.IOException; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.List; +import java.util.Locale; +import java.util.Map; + +import javax.swing.JInternalFrame; + +import org.testng.Assert; +import org.testng.AssertJUnit; +import org.testng.annotations.BeforeClass; +import org.testng.annotations.Test; + import jalview.analysis.scoremodels.SimilarityParams; import jalview.api.AlignViewportI; import jalview.api.AlignmentViewPanel; @@ -34,9 +50,13 @@ import jalview.api.FeatureColourI; import jalview.api.ViewStyleI; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; +import jalview.datamodel.DBRefEntry; +import jalview.datamodel.GeneLocus; import jalview.datamodel.HiddenSequences; +import jalview.datamodel.Mapping; import jalview.datamodel.PDBEntry; import jalview.datamodel.PDBEntry.Type; +import jalview.datamodel.Sequence.DBModList; import jalview.datamodel.SequenceCollectionI; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; @@ -67,25 +87,11 @@ import jalview.schemes.RNAHelicesColour; import jalview.schemes.StrandColourScheme; import jalview.schemes.TCoffeeColourScheme; import jalview.structure.StructureImportSettings; +import jalview.util.MapList; import jalview.util.matcher.Condition; import jalview.viewmodel.AlignmentViewport; import jalview.viewmodel.seqfeatures.FeatureRendererModel; -import java.awt.Color; -import java.io.File; -import java.io.IOException; -import java.util.ArrayList; -import java.util.HashMap; -import java.util.List; -import java.util.Map; - -import javax.swing.JInternalFrame; - -import org.testng.Assert; -import org.testng.AssertJUnit; -import org.testng.annotations.BeforeClass; -import org.testng.annotations.Test; - @Test(singleThreaded = true) public class Jalview2xmlTests extends Jalview2xmlBase { @@ -115,7 +121,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase af.getViewport() .getGlobalColourScheme() instanceof RNAHelicesColour, "Couldn't apply RNA helices colourscheme"); - assertTrue(af.saveAlignment(tfile, FileFormat.Jalview), + af.saveAlignment(tfile, FileFormat.Jalview); + assertTrue(af.isSaveAlignmentSuccessful(), "Failed to store as a project."); af.closeMenuItem_actionPerformed(true); af = null; @@ -153,11 +160,11 @@ public class Jalview2xmlTests extends Jalview2xmlBase assertNotNull( ColourSchemeProperty.getColourScheme(viewport, viewport.getAlignment(), - viewport.getGlobalColourScheme() - .getSchemeName()), + viewport.getGlobalColourScheme().getSchemeName()), "Recognise T-Coffee score from string"); - assertTrue(af.saveAlignment(tfile, FileFormat.Jalview), + af.saveAlignment(tfile, FileFormat.Jalview); + assertTrue(af.isSaveAlignmentSuccessful(), "Failed to store as a project."); af.closeMenuItem_actionPerformed(true); af = null; @@ -203,7 +210,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase sg.addSequence(af.getViewport().getAlignment().getSequenceAt(1), false); sg.addSequence(af.getViewport().getAlignment().getSequenceAt(2), true); af.alignPanel.alignmentChanged(); - assertTrue(af.saveAlignment(tfile, FileFormat.Jalview), + af.saveAlignment(tfile, FileFormat.Jalview); + assertTrue(af.isSaveAlignmentSuccessful(), "Failed to store as a project."); af.closeMenuItem_actionPerformed(true); af = null; @@ -441,9 +449,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase Assert.assertEquals(Desktop.getAlignFrames().length, Desktop.getAlignmentPanels( af.getViewport().getSequenceSetId()).length); - Assert.assertEquals( - Desktop.getAlignmentPanels( - af.getViewport().getSequenceSetId()).length, + Assert.assertEquals(Desktop + .getAlignmentPanels(af.getViewport().getSequenceSetId()).length, oldviews); } @@ -796,6 +803,11 @@ public class Jalview2xmlTests extends Jalview2xmlBase "Mismatch PDBEntry 'Type'"); Assert.assertNotNull(recov.getFile(), "Recovered PDBEntry should have a non-null file entry"); + Assert.assertEquals( + recov.getFile().toLowerCase(Locale.ENGLISH) + .lastIndexOf("pdb"), + recov.getFile().length() - 3, + "Recovered PDBEntry file should have PDB suffix"); } } @@ -838,13 +850,16 @@ public class Jalview2xmlTests extends Jalview2xmlBase /* * create a group with Strand colouring, 30% Conservation * and 40% PID threshold + * (notice menu action applies to selection group even if mouse click + * is at a sequence not in the group) */ SequenceGroup sg = new SequenceGroup(); sg.addSequence(al.getSequenceAt(0), false); sg.setStartRes(15); sg.setEndRes(25); av.setSelectionGroup(sg); - PopupMenu popupMenu = new PopupMenu(af.alignPanel, null, null); + PopupMenu popupMenu = new PopupMenu(af.alignPanel, al.getSequenceAt(2), + null); popupMenu.changeColour_actionPerformed( JalviewColourScheme.Strand.toString()); assertTrue(sg.getColourScheme() instanceof StrandColourScheme); @@ -981,7 +996,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase File tfile = File.createTempFile("JalviewTest", ".jvp"); tfile.deleteOnExit(); String filePath = tfile.getAbsolutePath(); - assertTrue(af.saveAlignment(filePath, FileFormat.Jalview), + af.saveAlignment(filePath, FileFormat.Jalview); + assertTrue(af.isSaveAlignmentSuccessful(), "Failed to store as a project."); /* @@ -1023,7 +1039,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase assertEquals(fr.getFeatureFilter("type2").toStableString(), "(Score LE 2.4) AND (Score GT 1.1)"); assertEquals(fr.getFeatureFilter("type3").toStableString(), - "(AF Contains X) OR (CSQ:PolyPhen NE 0.0)"); + "(AF Contains X) OR (CSQ:PolyPhen NE 0)"); } private void addFeature(SequenceI seq, String featureType, int score) @@ -1179,4 +1195,83 @@ public class Jalview2xmlTests extends Jalview2xmlBase .getAlignViewport(), "Didn't restore correct view association for the PCA view"); } + + /** + * Test save and reload of DBRefEntry including GeneLocus in project + * + * @throws Exception + */ + @Test(groups = { "Functional" }) + public void testStoreAndRecoverGeneLocus() throws Exception + { + Desktop.instance.closeAll_actionPerformed(null); + String seqData = ">P30419\nACDE\n>X1235\nGCCTGTGACGAA"; + AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(seqData, + DataSourceType.PASTE); + assertNotNull(af, "Didn't read in the example file correctly."); + + AlignmentViewPanel ap = Desktop.getAlignmentPanels(null)[0]; + SequenceI pep = ap.getAlignment().getSequenceAt(0); + SequenceI cds = ap.getAlignment().getSequenceAt(1); + + /* + * give 'protein' a dbref to self, a dbref with map to CDS, + * and a dbref with map to gene 'locus' + */ + DBRefEntry dbref1 = new DBRefEntry("Uniprot", "1", "P30419", null); + pep.addDBRef(dbref1); + Mapping cdsmap = new Mapping(cds, + new MapList(new int[] + { 1, 4 }, new int[] { 1, 12 }, 1, 3)); + DBRefEntry dbref2 = new DBRefEntry("EMBLCDS", "2", "X1235", cdsmap); + pep.addDBRef(dbref2); + Mapping locusmap = new Mapping(null, + new MapList(new int[] + { 1, 4 }, new int[] { 2674123, 2674135 }, 1, 3)); + DBRefEntry dbref3 = new GeneLocus("human", "GRCh38", "5", locusmap); + pep.addDBRef(dbref3); + + File tfile = File.createTempFile("testStoreAndRecoverGeneLocus", + ".jvp"); + try + { + new Jalview2XML(false).saveState(tfile); + } catch (Throwable e) + { + Assert.fail("Didn't save the state", e); + } + Desktop.instance.closeAll_actionPerformed(null); + + new FileLoader().LoadFileWaitTillLoaded(tfile.getAbsolutePath(), + DataSourceType.FILE); + AlignmentViewPanel rap = Desktop.getAlignmentPanels(null)[0]; + SequenceI rpep = rap.getAlignment().getSequenceAt(0); + DBModList dbrefs = rpep.getDBRefs(); + assertEquals(rpep.getName(), "P30419"); + assertEquals(dbrefs.size(), 3); + DBRefEntry dbRef = dbrefs.get(0); + assertFalse(dbRef instanceof GeneLocus); + assertNull(dbRef.getMap()); + assertEquals(dbRef, dbref1); + + /* + * restored dbrefs with mapping have a different 'map to' + * sequence but otherwise match the original dbrefs + */ + dbRef = dbrefs.get(1); + assertFalse(dbRef instanceof GeneLocus); + assertTrue(dbRef.equalRef(dbref2)); + assertNotNull(dbRef.getMap()); + SequenceI rcds = rap.getAlignment().getSequenceAt(1); + assertSame(dbRef.getMap().getTo(), rcds); + // compare MapList but not map.to + assertEquals(dbRef.getMap().getMap(), dbref2.getMap().getMap()); + + /* + * GeneLocus map.to is null so can compare Mapping objects + */ + dbRef = dbrefs.get(2); + assertTrue(dbRef instanceof GeneLocus); + assertEquals(dbRef, dbref3); + } }